The answer you wanted was “We analysed the laminin that the cells had deposited.”
Use ‘that’ whenever it is a necessary part of the sentence, and when you would not pause before it in speech (Essential or restrictive clauses).
If it simply is a break before giving fresh information, and you would pause before it in speech, use ‘which’ (or ‘who’) with a preceding comma (Non-essential or non-restrictive clause.)
“We quantified the deposited laminin, which was assembled into rose-like patterns.” Here, the patterns were not part of the quantification so it’s just an interesting aside!
In case you don’t know… Laminins are awesome! They are a family of proteins that hold your tissues together.